MolNFT v1 · #150021 · protein
Structural analysis of the ternary complex between lamin A/C, baf and emerin identifies an interface disrupted in autosomal recessive progeroid diseases
6GHD: “Structural analysis of the ternary complex between lamin A/C, baf and emerin identifies an interface…”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.39). MolNFT v1 #150021 on GenesisL1: 3D structure, binding…
- PDB
- 6GHD
- Type
- protein
- Length
- 675 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Emerin; Barrier-to-autointegration factor; Prelamin-A/C
- UniProt
- P50402, O75531, P02545
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.39
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Emerin | protein | 45 | 58% helix, 0% strand | P50402 |
| D, C | Barrier-to-autointegration factor | protein | 87 | 68% helix, 2% strand | O75531 |
| B | Prelamin-A/C | protein | 119 | 3% helix, 50% strand | P02545 |
| E, A | Barrier-to-autointegration factor | protein | 88 | 67% helix, 2% strand | O75531 |
| F | Prelamin-A/C | protein | 118 | 3% helix, 51% strand | P02545 |
| H | Emerin | protein | 43 | 53% helix, 0% strand | P50402 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains G, D, E, A, C, H
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.39 | 0.73 | 24 | empty |
| 2 | 111 | 0.36 | 0.73 | 20 | empty |
| 3 | 84 | 0.32 | 0.74 | 15 | empty |
| 4 | 52 | 0.29 | 0.76 | 15 | empty |
| 5 | 65 | 0.29 | 0.74 | 18 | empty |
Interfaces
14 interfaces between chains.
- D–E · 757 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 755 Ų buried · 10 hydrogen bonds · protein-protein
- G–D · 406 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 405 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 297 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6GHD · Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies… · the same entry in another collection · chain H against H, TM-score 1.00
- P02545 · AlphaFold monomer V2.0 prediction for prelamin-A/C (P02545) · a predicted model of the same protein · chain F against A, TM-score 0.99
- O75531 · AlphaFold monomer V2.0 prediction for barrier-to-autointegration factor (O75531) · a predicted model of the same protein · chain D against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P50402
- Every structure of UniProt O75531
- Every structure of UniProt P02545
- Elsewhere: RCSB PDB 6GHD · PDBe 6GHD · UniProt P50402 · UniProt O75531 · UniProt P02545
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